They are there for two reasons:
1. They should help shield RFI (radio frequency interference).
2. They protect the boot from radiative heat transfer from the exhaust manifold.
A note on heat transfer. Classically there are three types, radiative, conductive and convective. Convective heat transfer doesn't really apply here, so we'll ignore it.
When most of us think of hot things, we think of conductive heat transfer. That type of heat transfer happens when things touch each other. For example, put hand on radiator, hand gets hot. Using OP's example, handle spark plugs protectors after running the engine, hand gets hot.
Radiative heat transfer is a different animal. This happens when certain items get REALLY hot, hot enough to glow (radiate). Classic examples would be a large bonfire that can burn your face even though you may be standing several feet away and the air is near freezing. The Sun is also an example of this. It's a giant H-bomb that radiates so much heat that it can burn you from 93 million miles away. Under our hood, the only component that gets hot enough to radiate is the exhaust manifolds. If you put in headers, you get even more radiation.
The protection against radiation is a shield that the radiation can't penetrate. If you look around your exhaust manifold, you'll see all kinds of shiny thin shields. They aren't thick, and they don't have fluffy-type insulation. They are designed for one thing -- to protect components against radiative heat. The exhaust manifold shield is one of the first lines of defense. You'll also see shiny shielding on wire bundles, on the firewall, and, of course, the boot shields that OP refers to.
Short term, you'll be fine without them. But, long term, you want to protect against this heat. It will definitely shorten the lifespan of the component.
On my header install, I did a couple of things:
1. Ceramic coating on the Kooks Mids. Shiny ceramic coating is an awesome way to shield that radiation.
2. Used some trick Accel wires that have shiny-white ceramic boots.
'09 GT, Vararaam, Kooks Mids + GXP Muffs, Cortex 91, Enkei PF01+Michelin Pilot SS (43lbs per corner!!)